rs4978617

Positions:

• chr9-115002569-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649121.1(DELEC1):​n.78+32908C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,098 control chromosomes in the GnomAD database, including 29,750 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (29750 hom., cov: 32)
• Consequence: DELEC1 ENST00000649121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

Genes affected

DELEC1 (HGNC:23658): (deleted in esophageal cancer 1) The function of this gene is not known. This gene is located in a region commonly deleted in esophageal squamous cell carcinomas. Gene expression is reduced or absent in these carcinomas and thus this is a candidate tumor suppressor gene for esophageal squamous cell carcinomas. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DELEC1	ENST00000649121.1	n.78+32908C>T		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000648852.1	n.276+32908C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93496 AN: 151978 Hom.: 29738 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.580

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.615 AC: 93549 AN: 152098 Hom.: 29750 Cov.: 32 AF XY: 0.616 AC XY: 45796 AN XY: 74366

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.583

Alfa AF: 0.649 Hom.: 5571

Bravo AF: 0.589

Asia WGS AF: 0.644 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.8
DANN	Benign	0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4978617; hg19: chr9-117764849; COSMIC: COSV60395732;